Figure 4

Cluster analysis of hdac1 mutant and morphant transcriptomes identifies a core set of Hdac1-regulated genes. The Cluster Tree displays the relationships between transcriptomes of 27 hpf hdac1 mutant embryos and 12 hpf, 18 hpf and 27 hpf Hdac1ATG1 morphant embryos. The threshold for statistically significant differential expression was set at p <10^-5 for all probes and an additional >2-fold-change criterion was then applied to identify a subset of 84 probes whose expression was changed in Hdac1ATG1 morphants at all three times points (Suppl. Table S2). To eliminate probes from this group that did not exhibit altered expression in the 27 hpf hdac1 mutant samples, an exclusion criterion was then applied to eliminate probes that did not exhibit a >1.2-fold change in transcript abundance in 27 hpf hdac1 mutants in comparison to controls. Thus, 67 probes were identified that exhibited a >2-fold change in transcript abundance in Hdac1ATG1 morphants at 12 hpf, 18 hpf and 27 hpf and a >1.2 fold change in transcript abundance in hdac1 mutants, in comparison to controls. All of these expression changes met the threshold for statistical significance of p < 10^-5. The expression changes for each of the listed genes are given for each of the individual microarrays analysed. Up-regulated probes are indicated in red; down-regulated probes are indicated in green. The samples include 8 hdac1 mutant/wild-type sibling replicates, plus biological triplicates for each of the 12 hpf, 18 hpf and 27 hpf Hdac1ATG1/Standard Control morphant comparisons (see Methods section for further details). Genes that are expressed in the CNS or have a CNS-oriented function are indicated in orange.